Behe’s B-Cell Bravado, Part 3: Failure to Engage the Evidence

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July 7, 2010 Tags: Genetics

Today's entry was written by Kathryn Applegate. You can read more about what we believe here.

Behe’s B-Cell Bravado, Part 3: Failure to Engage the Evidence

Many non-scientists are unaware of the importance or extent of “the scientific literature.” In the geeky world of science, success doesn’t depend on social prowess or earning power (thankfully!), but on one’s publication record. It’s hard to get published—to do so means making a significant contribution to the field, as judged by a panel of anonymous reviewers. Most people have nightmares about being chased or drowning. Scientists have nightmares about their papers getting rejected.

The main database for accessing the biomedical research papers, called PubMed, contains over 19 million articles. If you search PubMed for irreducible complexity, you’ll get 11 hits, none of which represents a peer-reviewed piece of work showing evidence of an Intelligent Designer. Most of the hits are commentaries on the Intelligent Design (ID) movement itself or attempts to “reduce” irreducible complexity. A couple of them are totally irrelevant.

Could this mysterious absence from the literature be a result of a conspiracy by Big Science to deliberately marginalize the work of people like Michael Behe? Though ID proponents often try to make this case (just watch Ben Stein’s Expelled), I think it’s very, very unlikely. But let’s give them the benefit of the doubt. If ID theory is scientific in nature, we can expect its leaders to engage scrupulously—as all scientists must—with the literature.

Unfortunately, Michael Behe does not have a great track record in this department. Consider his 1996 book Darwin’s Black Box. When reading the chapter on the immune system, for example, I kept expecting him to interact with the evidence for the gradual development of the antibody recombination system. The transposon hypothesis, which we examined in detail in Part 2, is a well-tested model for how this system could have originated. I couldn’t wait to see what Behe would say about it! His response was more than a little disappointing. He does refer to the model, at least indirectly, but only by discounting a two-page commentary—the purported “best efforts” in the field—as mere speculation:

[The authors] make a valiant stab at accounting for the components [of the antibody diversity generation system], but in the end, it is a hop in the box with Calvin and Hobbes. The authors speculate that a gene from a bacterium might have luckily been transferred to an animal. Luckily, the protein coded by the gene could itself rearrange genes; and luckily, in the animal’s DNA there were signals that were near antibody genes; and so on. In the final analysis the authors identify key problems with gradualistic evolution of the immune system, but their proffered solutions are really just a disguised shrug of their shoulders (137).

Seriously, a hop in the box with Calvin and Hobbes? If you search Pubmed for RAG transposon, you’ll get 18 hits, and they’re all relevant to the evolution of the immune system. More papers deal directly with the data for the transposon hypothesis than for the much broader topic of irreducible complexity! The top two hits are recent reviews, each of which cites dozens of papers. And the first paper ever to propose the transposon hypothesis (Sakano et al. Nature 1979, which doesn’t even appear in this narrow search) has been cited hundreds of times in peer-reviewed publications.

Questions certainly remain about the details of the transposon model, but Behe makes it sound like a pie in the sky idea with no supporting data. He writes, “We can look high or we can look low, in books or in journals, but the result is the same. The scientific literature has no answers to the question of the origin of the immune system” (138). This is patently false. Behe may not like the answers, but he misleads the public when he suggests they don’t exist.

Nearly 15 years have passed since Darwin’s Black Box first came out. During that time, scientists have collected some of the most compelling evidence for the transposon hypothesis (see Part 2). What has Behe said about this new data?

In 2005, he testified in a now-famous Dover, Pennsylvania, courtroom in favor of teaching ID alongside evolution in public schools. Behe maintained his previous position: “The scientific literature has no detailed testable answers on how the immune system could have arisen by random mutation and natural selection.”

The judge, John E. Jones, wrote in his decision that Behe “was presented with 58 peer-reviewed publications, nine books, and several immunology textbook chapters about the evolution of the immune system; however, he simply insisted that this was still not sufficient evidence of evolution…” Jones ultimately ruled against teaching ID in classrooms, in part because of the impossibly high burden of proof Behe demanded. In 2006, the 10th anniversary edition of Darwin’s Black Box appeared, featuring a new afterword. While Behe cleared up a few apparent misconceptions about irreducible complexity, he stood by the original text as a whole:

Despite the enormous progress of biochemistry in the intervening years, despite hundreds of probing commentaries…,despite implacable opposition from some scientists at the highest levels, the book’s argument for design stands. Other than updating the list of my children in the Acknowledgements…there is very little of the original text I would change if I wrote it today (255).

Specifically about the immune system, Behe mentioned one new paper from 2005, but only to reemphasize that nothing in his thinking had changed:

Whatever interesting things [the 2005 paper] speculated about gradual evolution, however, it had nothing to say about Darwinian evolution. In fact neither Darwin’s name nor any derivative word appeared in the paper. Nor did the phrase “natural selection” appear; “selection” is used once.” “Mutation” appears twice, but the envisioned mutations are not specified (269).

This sort of defense is peculiar. Behe counts words when he should be grappling with the data. Interestingly, he implicitly admits that a gradual evolutionary process may be sufficient to explain the origin of the irreducibly complex immune system, but he contrasts such a process with Darwinian evolution, by which he means mutation and natural selection.

Recall the quote I referenced in my last post, in which Behe lays out the criteria for detecting design:

The laws of nature can organize matter…The most relevant laws are those of biological reproduction, mutation, and natural selection. If a biological structure can be explained in terms of those natural laws, then we cannot conclude that it was designed. Throughout this book, however, I have shown why many biochemical systems cannot be built up by natural selection working on mutations: no direct, gradual route exists to these irreducibly complex systems… (203).

The transposon hypothesis outlines a possible gradual route to an irreducibly complex system, and it relies entirely on the laws of reproduction, mutation, and natural selection. Nevertheless, Behe remains unconvinced. In his mind, to explain the origin of an irreducibly complex system entirely in terms of natural laws, one would have to show that the steps were in fact unguided.

Such a requirement can be seen more clearly in his 2009 letter to the editor at Science, written in response to a news focus article about the origins of the immune system. Science chose not to publish the letter, so Behe posted it on the ID blog Uncommon Descent. He wrote:

Darwin’s chief contribution was not the simple idea of common descent, but the hypothesis that evolution is driven completely by ateleological mechanisms, prominently including random variation and natural selection. Intelligent design has no proper argument with the bare idea of common descent; rather, it disputes the sufficiency of ateleological mechanisms to explain all facets of biology…

Many scientists agree with Behe that evolution may have been guided in some mysterious way by a Mind. But whether or not the methods of science could ever rigorously detect teleology—mindful purpose—by studying the physical world is hotly debated. Most working scientists I know do not believe science is equipped for such a task.

Questions about teleology are fascinating, but today I’m concerned with just one thing: whether or not Behe has sufficiently engaged with the scientific literature. If I had read his book without any prior knowledge of immunology (or the other topics he covers), I’m pretty sure I would be left with a deep distrust of scientists and the scientific process. I think that’s a pity.

Kathryn Applegate is Program Director at The BioLogos Foundation. She received her PhD in computational cell biology at The Scripps Research Institute in La Jolla, Calif. At Scripps, she developed computer vision software tools for analyzing the cell's infrastructure, the cytoskeleton.

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Stephen Matheson - #23020

July 22nd 2010

So…. Bill wasn’t banned for writing those things. You just thought you’d bring them up to show what “offensive” behavior at UD looks like. I found that astounding even before Bill provided the nauseating context.

You’re inviting me to come to your site for discussion. But you seem not to understand why I don’t trust you. One way to help me along would be to comment on some of the more obnoxious performances in the “discussion” of my blog posts on your site last month. Here are some nice samples.

I’m quite curious about the means by which you judge civility on your site after reading those threads.

And no, I’m not interested in visiting your site as a “contributor” given your stunning confusion about “civility” and discourse. If you can read those threads without repeatedly thinking “mockery, plain and simple”... then there’s something seriously wrong with your integrity. “Honest and sincere discussion?” Really, Clive? Really?!?

Mark Frank - #23039

July 23rd 2010

Clive - as you are monitoring this debate and it seems to have become a discussion about posting on UD - can you help?  I just want to know if I have been banned or not!

I have been unable to post on UD for several weeks (my comments simply do not appear). I could see no reason why I should be banned and there was no explanation.  I thought it was a technical problem so I tried using a different computer, a different IP address and created a new id (but made it clear it was me).  I was still unable to comment.

Can you advise?



Maya - #23044

July 23rd 2010


My suspicion is that Clive is a performance artist.  He carefully controls the number of reality-based posters on UD in order to keep the ID supporters in a state of maximum posting frenzy.  Too many scientifically literate posters and the ID supporters get soundly trounced and leave for safer venues.  Too few and the ID supporters have only themselves to talk to, and even they start to realize how ridiculous the people they share their big tent with sound.

I’m sure he’ll let you back once he decides that Petrushka can serve his purpose better by being banned than being allowed to post.

The alternative, that Clive could really be that much of a coward and hypocrite and still look himself in the mirror every morning, is simply too depressing to consider.

Clive Hayden - #23132

July 23rd 2010

Mark Frank,

It looks like you have three accounts, so to avoid confusion, I narrow it down to one account for use by putting the rest in the banned filter. So you can use your mark.t.frank account. It makes it easier when people use only one account. I’ve seen the same person using different names and different accounts, so to make it easy, just use one account at a time please. But you’re free to post under the account mentioned above.

Clive Hayden - #23136

July 23rd 2010

Reciprocating Bill,

——-“You did not. However, in response to my imagining StephenB muttering on a park bench, you banned me. Your actions (and lack thereof) speak for themselves.”

Again, No, old friend, those comments from Diffaxial prompted me to investigate, and that’s when I discovered you had been banned before. I brought your comments up on this post to show that you aren’t as civil and as interested in following the moderation policies as you claim to be. StephenB has nothing to do with that little contradiction. But that is not why I banned Diffaxial, I banned that sock puppet for being a banned sock puppet before.

Clive Hayden - #23146

July 23rd 2010

Stephen Matheson,

You did not contribute, old friend, even when I invited you. Had you, no one would’ve been uncivil towards you or your comments. Will you, now, come to UD, and we can discuss things? I’ll even start a thread dedicated to you. I’ll make sure that the discussion is very civil. If I do not, you’re more than welcome to call me out on it, at UD and at your own blog or wherever you would like to. Will you please come to Uncommon Descent and we can talk about it?

Reciprocating Bill - #23175

July 23rd 2010


I brought your comments up on this post to show that you aren’t as civil and as interested in following the moderation policies as you claim to be.

Clive, are you really that oblivious to what just happened? Wow.

The force of my last post is that it illustrates the hypocrisy of your claim to be interested in “civility” in your moderation. Proponents of ID repeatedly call others liars, cowards, incapable of rationality, etc., and you remain silent.

Your reasons for banning Diffaxial have no bearing upon that.

BTW, why do you address me as “old friend?” Strikes me as, well, insincere.


Reciprocating Bill - #23178

July 23rd 2010

StephenB on respect, same thread:

“Why you would invest all those paragraphs to run a bluff is beyond me. Everything you write is a bluff wrapped up in a fog. You promised that you would defend your irrational position just once, and my respectful tone was contingent on the anticipation that you would follow through with that promise. So, you can be sure that the short lived attempt to be respectful has more than run its course. You didn’t deliver…you simply launched into another one of your irrational screeds, and it is irrational in all respects…you slink away from your own promise, knowing that you can’t back it up and return to your usual nonsensical perspective on logic.”

“One of the reasons I wrote the second paragraph was to insure that there is no misunderstanding…given the Darwinist capacity to do what you are currently doing, that is, lie about what was said…”

“I don’t hesitate to says that you are both dishonest.”

“Any possible ambiguity is eliminated by the second paragraph, which both of you consistently leave out. That makes both of you dishonest.

“I used the opportunity to dramatize you irrationality about causeless physical events, which is, of course, your calling card.”


Stephen Matheson - #23190

July 23rd 2010


You seem to be moving the goalposts. You claim that no one would have been uncivil to me if had been a “contributor.” I conclude: 1) civility is not the value you claim it to be, since you seem to adjust the standards based on whether someone is a “contributor” and 2) you’re confused about the timeline of our interaction. The most obviously disgusting example of uncivil behavior occurred well before you even discussed “inviting” me to your place.

Seriously, Clive, this is really basic stuff. You’re trying to claim the moral high ground for a website that is justifiably notorious for its myriad abuses of standards of reasoned discourse (not to mention basic moral conduct). If you want to rehabilitate your site’s image, you need to start by acknowledging its many problems. That alone would earn you a little more trust from me, and would move us a little closer to the discussion you claim to seek.

Reciprocating Bill - #23268

July 24th 2010

The Wisdom of Upright Biped:

“So if you are, perhaps, a slow learner or have difficulty with modest conceptualizations, then I simply did not pick up on it. More than likely I may have overlooked it given your pompous certainty… I apologize for not being more empathetic to any special needs you might have.… I simply assumed that you were just another materialist bigot… I am more than willing to slow down for you.”

“As it becomes obvious, Diffaxial cannot allow himself the burden that he might be wrong – even to the extent of being able to have a reasoned conversation about the possibilities. He is a coward in this regard.”

“This is an out and out lie. You are now lying to make your point.” (I subsequently ignored all of Biped’s comments.)

On a thread started by Clive:

“That was the most baited and sophmoric attempt witnessed since the recent talking donkey episodes (or perhaps watching Diffaxial’s laborious and repeated sholveling of the ground under his feet).”

“I think that all regulars at this site have come to understand that Diffaxial cannot say anything in which he does not assume his conclusion. It is, apparently, a pathological trait from which he has chosen not to allay himself.”


Reciprocating Bill - #23269

July 24th 2010

The Wisdom of Upright Biped, continued:

“Why would you ask such an ignorant and misplaced (dumbassed) question? Was it meaningful to you in some fashion personally?”

“The glaring difference between our positions is that I rationally incorporate what we observe in nature, while you irrationally ignore it.”

“In other words, [Diffaxial’s] response was a nonsensical load of crap. Which was then immediately followed by a return to obfuscation.”

“In Diffaxial’s case, he was simply a fool.”

“Diffaxial, try to make sense – and try to be consistent as well.”

As Clive did not remark upon any of these comments, including one that occurred on a thread he initiated, we can infer that they comport with his deep concern with “civility.”

gingoro - #23280

July 24th 2010

Stephen Matheson @22961

“My only suggestion is this: stop pretending that your policy advances or values civility.”

I suspect that they do value civility but that there are other policies that are not talked about that take precedence.  If I were to refer to one of their headline posters as a “white ape”, probably I would get banned as well.  Of course it is their site they can ban who ever they want to for no apparent reason. 

When George Murphy was banned it was for a suggestion that ID and UcD were wasting their time.  I think the current moderators need to look and see exactly why people were banned and not just uphold the decisions of the past moderators which IMO often were not justified. 

Dave W
PS (In the late 1800s we dirty Irish were called white apes by an Anglician commission looking at the famine problem.  My mother was of Irish and German extraction and even in the late 1930s was referred to as dirty Irish in the home of future inlaws)

Reciprocating Bill - #23290

July 24th 2010

The remark that resulted in George Murphy’s banning:

I don’t think you guys realize how insular your discussions are. This blog as a whole reminds me of a bunch of kids playing D & D. It may be a fun & harmless way to spend a Saturday afternoon, but it’s kind of sad if they think that it has anything to do with the real world.

gingoro - #23293

July 24th 2010

Gregory @22977

I think you comments about Matheson are over the top and uncalled for.  As best I read about what happened at the Biola conference with ID, Steve and the other none ID scientist were not well treated by the DI. 
Dave W

Gregory - #23298

July 24th 2010

No idea about what you’re talking about wrt Biola conference, gingoro. You’re the first to raise it in the thread.

Do you deny that many biologists ‘run away’ when asked about the *ideology of evolutionism*, i.e. that which makes MANY people doubt biology because of guilt by association?

It’s happened here and at ASA, but you don’t want to be a fair reporter of things, it appears.

Rich has said similar things about Matheson here. Why not scold him too?

Btw, do you think Behe is a ‘sad figure’ like Matheson does (above)?

gingoro - #23305

July 24th 2010

Gregory @23298

No public comment!

Gregory - #23306

July 24th 2010

Yes, exactly, Dave.

Reciprocating Bill - #23549

July 26th 2010

The following magical moments of civility, UD style, passed muster with Clive just today:


“Petrushka has been puking all over him or herself throughout this thread. If you or upright were damned by your own words the both of you would be embarrassed . Petrushka on the other hand is either to dumb or just to dishonest to know or care.”

“What lessons have we learned so far?

1)That both Gaz and Petrushka embrace irrationality”

2) The second lesson is that, either by comission or omission, neither one of them are truly interested in the truth…

3) Finally the third lesson we can take from all this is that they are intellectually dishonest. Observe th smoke screens, the back tracking , the dodging, the obfuscations as evidenced by their refusal to answer direct questions. Questions that they know will damn themselves if they do. This is not the sign of an intellectually honest person.”

It is any wonder Clive has fled this discussion?

Reciprocating Bill - #23555

July 26th 2010

Still more UD civility:

“Earth to Gaz??? Are you there Gaz? ...

I think you are losing it Gaz understandably so. If I got asbeatup as you have on this thread I would be punch drug as well.



Maya - #23676

July 27th 2010

It appears that Clive is hiding behind his own skirts at UD, rather than addressing the evidence of his hypocrisy here.  Neat trick, that.

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